Lecture 3: Classification of living organisms

Question 1

What did Beijerink and Winogradsky do?

Answer 1

They introduced the enrichment-culture technique and the use of selective media to ensure that the desired microorganisms could grow the best.

Question 2

What are the two ways of classifying living organisms? Which is currently used?

Answer 2

Phylogeny and taxonomy. Phylogeny is currently used.

Question 3

What is the difference between taxonomy and phylogeny?

Answer 3

Taxonomy is an artificial classification system of living organisms solely based on visible similarities and fossils, but that is still used to name organisms. Phylogeny is the natural classification of organisms based on their evolutionary relatedness.

Question 4

When did microorganisms become a category of organisms considered in taxonomy? Why did it take so long?

Answer 4

They only started being considered in the late 1960s, because there are no microbial fossils to refer to and all have very similar shapes.

Question 5

How was the transition from taxonomy to phylogeny finally made?

Answer 5

A ubiquitous gene sequence was used to compare organisms (including microorganisms) and a universal phylogenetic tree of life could be constructed.

Question 6

What groups of organisms were initially considered in early classification schemes of living organisms before 1866?

Answer 6

The only groups considered were plants and animals.

Question 7

When and by whom were microorganisms first proposed to be included in early classification schemes of living organisms?

Answer 7

They were initially proposed to be added to plants and animals by Ernest Haeckel in 1866.

Question 8

What were the kingdoms of life according to Haeckel’s tree of life? Where were microorganisms placed?

Answer 8

The kingdoms of life were plants, animals, and protists (which is where all the microorganisms were placed).

Question 9

By whom and when was Haeckel’s proposal challenged? What discovery drove this challenge?

Answer 9

Chatton in 1937, with the discovery of eucaryotes and procaryotes, which have different types of cells.

Question 10

Whose classification scheme followed Haeckel’s? What were the kingdoms of life included in it?

Answer 10

Whittaker in 1959. It included monera, protista, fungi, plantae, and animalia.

Question 11

Explain the layout of Whittaker’s five kingdom classification (including where bacteria fit into it). Was it correct?

Answer 11

The common ancestor was seen as monera (which included bacteria), which gave rise to protista, which then split off into plantae, fungi, and animalia. This was completely wrong.

Question 12

What classification scheme followed Whittaker’s and when? How was it created?

Answer 12

Woese’s scheme followed in 1977. It was based on the sequencing of the 16S ribosomal RNA gene, which all organisms have as a component of the ribosome.

Question 13

Describe Woese’s classification scheme.

Answer 13

It consisted 3 kingdoms: Bacteria, Archaea, and Eucaryotes, that are equally distant and that come from a common ancestor.

Question 14

Name the 5 steps involved in building a phylogenetic tree.

Answer 14

1. Get a sequence of a ubiquitous gene, which will serve as the phylogenetic marker
2. Align the gene sequences using a program
3. Feed the aligned sequences to a phylogenetic algorithm
4. Determine which sequences are the most homologous and link the closest neighbours
5. Create the phylogenetic tree

Question 15

What is the endosymbiotic theory of evolution?

Answer 15

It is the theory that a primitive eucaryotic cell engulfed an ancient procaryote to create the first true eucaryotic cell.

Question 16

Explain (in general) the justification behind the endosymbiotic theory of evolution.

Answer 16

Procaryotes do not contain organelles, but nearly all eucaryotes do. Plants and algae have mitochondria and chloroplasts, while all other eucaryotes only have mitochondria. Given that mitochondria and chloroplasts resemble procaryotes, the idea is that the organelles are derived from engulfed procayotic cells.

Question 17

Name 5 ways in which mitochondria and chloroplasts resemble procaryotes.

Answer 17

1. They are approximately the same size
2. They are the only organelles containing DNA like pracaryotes do
3. They both contain circular genomes
4. They contains similarly sized ribosomes (70S vs 80S)
5. Both have double membrane
6. They multiple and divide by binary fission

Question 18

Describe the mutually beneficial relationship between the primitive eucaryotic cell and the ancient prokaryote in the endosymbiotic theory.

Answer 18

The procaryotic cell benefited from having a sheltered environment rich in nutrients, which the eucaryotic cell benefited from containing an organism that produced energy (ATP).

Question 19

Did the engulfment of the procaryote responsible for the mitochondria and the procaryote responsible for the chloroplast occur at the same time? Explain why or why not.

Answer 19

No, the engulfment of the procaryote that later became the chloroplast happened later, because while all eukaryotes have mitochondria, only a subset, plants, have a chloroplast.

Question 20

Who proposed the endosymbiotic theory?

Answer 20

Lynn Margulis

Question 21

According to Woess’ kingdom scheme, describe the sequence of evolution of prokaryotes, eukaryotes, and plants. Explain why we believe this.

Answer 21

Prokaryotes came first, around 4.5 billion years ago. Then eukaryotes evolved around 1 billion years ago. Plants came last at 0.7 billion years ago because they have chloroplasts, while the rest of eukaryotes don’t.

Question 22

Mitochondria are descendants of a […], while chloroplasts are descendants of a […]

Answer 22

Parasitic proteobacterium, cyanobacteria

Question 23

Is endosymbiosis an ongoing or finished process? Explain.

Answer 23

It is ongoing - eucaryotes constantly need to phagocytose new prokaryotes in order to co-evolve and create a stable organism.

Question 24

Give an example of more modern endosymbiosis.

Answer 24

Aphids and related insects (last 200 million years). Aphids are dependent of their endosymbiont, and one cannot live without the other. This is a stable endosymbiotic event.